__init__.py

# Copyright 2000 by Jeffrey Chang, Brad Chapman. All rights reserved.# Copyright 2006, 2007 by Peter Cock. All rights reserved.# This code is part of the Biopython distribution and governed by its# license. Please see the LICENSE file that should have been included# as part of this package."""Code to work with GenBank formatted files.Classes:Iterator Iterate through a file of GenBank entriesDictionary Access a GenBank file using a dictionary interface.ErrorFeatureParser Catch errors caused during parsing.FeatureParser Parse GenBank data in Seq and SeqFeature objects.RecordParser Parse GenBank data into a Record object.NCBIDictionary Access GenBank using a dictionary interface._BaseGenBankConsumer A base class for GenBank consumer that implements some helpful functions that are in common between consumers._FeatureConsumer Create SeqFeature objects from info generated by the Scanner_RecordConsumer Create a GenBank record object from Scanner info._PrintingConsumer A debugging consumer._Scanner Set up a GenBank parser to parse a record.ParserFailureError Exception indicating a failure in the parser (ie. scanner or consumer)LocationParserError Exception indiciating a problem with the spark based location parser.Functions:index_file Get a GenBank file ready to be used as a Dictionary.search_for Do a query against GenBank.download_many Download many GenBank records."""import cStringIO
# other Biopython stufffrom Bio.expressions import genbank
from Bio.ParserSupport import AbstractConsumer
import utils
#There used to be a (GenBank only) class _Scanner in#this file. Now use a more generic system which we import:from Scanner import GenBankScanner as _Scanner
from Bio import Mindy
from Bio.Mindy import SimpleSeqRecord
from Bio import db
from Bio import EUtils
from Bio.EUtils import DBIds, DBIdsClient
#Constants used to parse GenBank header lines
GENBANK_INDENT = 12
GENBANK_SPACER = " " * GENBANK_INDENT
#Constants for parsing GenBank feature lines
FEATURE_KEY_INDENT = 5
FEATURE_QUALIFIER_INDENT = 21
FEATURE_KEY_SPACER = " " * FEATURE_KEY_INDENT
FEATURE_QUALIFIER_SPACER = " " * FEATURE_QUALIFIER_INDENT
00065class Dictionary:
"""Access a GenBank file using a dictionary-like interface. """00068def __init__(self, indexname, parser = None):
"""Initialize and open up a GenBank dictionary. Each entry is a full GenBank record (i.e. from the LOCUS line to the // at the end of the sequence). Most GenBank files have only one such "entry", in which case using this dictionary class is rather unnecessary. Arguments: o indexname - The name of the index for the file. This should have been created using the index_file function. o parser - An optional argument specifying a parser object that the records should be run through before returning the output. If parser is None then the unprocessed contents of the file will be returned. """
self._index = Mindy.open(indexname)
self._parser = parser
def __len__(self):
return len(self.keys())
def __getitem__(self, key):
# first try to retrieve by the base idtry:
seqs = self._index.lookup(id = key)
# if we can't do that, we have to try and fetch by aliasexcept KeyError:
seqs = self._index.lookup(aliases = key)
if len(seqs) == 1:
seq = seqs[0]
else:
raise KeyError("Multiple sequences found for %s" % key)
if self._parser:
handle = cStringIO.StringIO(seq.text)
return self._parser.parse(handle)
else:
return seq.text
def keys(self):
primary_key_retriever = self._index['id']
return primary_key_retriever.keys()
00114class Iterator:
"""Iterator interface to move over a file of GenBank entries one at a time. """00117def __init__(self, handle, parser = None):
"""Initialize the iterator. Arguments: o handle - A handle with GenBank entries to iterate through. o parser - An optional parser to pass the entries through before returning them. If None, then the raw entry will be returned. """
self.handle = handle
self._parser = parser
00128def next(self):
"""Return the next GenBank record from the handle. Will return None if we ran out of records. """if self._parserisNone :
lines = []
whileTrue :
line = self.handle.readline()
ifnot line : returnNone#Premature end of file?
lines.append(line)
if line.rstrip() == "//" : breakreturn"".join(lines)
try :
return self._parser.parse(self.handle)
except StopIteration :
returnNonedef __iter__(self):
return iter(self.next, None)
00149class ParserFailureError(Exception):
"""Failure caused by some kind of problem in the parser. """pass00154class LocationParserError(Exception):
"""Could not Properly parse out a location from a GenBank file. """pass00159class FeatureParser:
"""Parse GenBank files into Seq + Feature objects. """00162def __init__(self, debug_level = 0, use_fuzziness = 1,
feature_cleaner = utils.FeatureValueCleaner()):
"""Initialize a GenBank parser and Feature consumer. Arguments: o debug_level - An optional argument that species the amount of debugging information the parser should spit out. By default we have no debugging info (the fastest way to do things), but if you want you can set this as high as two and see exactly where a parse fails. o use_fuzziness - Specify whether or not to use fuzzy representations. The default is 1 (use fuzziness). o feature_cleaner - A class which will be used to clean out the values of features. This class must implement the function clean_value. GenBank.utils has a "standard" cleaner class, which is used by default. """
self._scanner = _Scanner(debug_level)
self.use_fuzziness = use_fuzziness
self._cleaner = feature_cleaner
00182def parse(self, handle):
"""Parse the specified handle. """
self._consumer = _FeatureConsumer(self.use_fuzziness,
self._cleaner)
self._scanner.feed(handle, self._consumer)
return self._consumer.data
00190class RecordParser:
"""Parse GenBank files into Record objects """00193def __init__(self, debug_level = 0):
"""Initialize the parser. Arguments: o debug_level - An optional argument that species the amount of debugging information the parser should spit out. By default we have no debugging info (the fastest way to do things), but if you want you can set this as high as two and see exactly where a parse fails. """
self._scanner = _Scanner(debug_level)
00204def parse(self, handle):
"""Parse the specified handle into a GenBank record. """
self._consumer = _RecordConsumer()
self._scanner.feed(handle, self._consumer)
return self._consumer.data
00211class _BaseGenBankConsumer(AbstractConsumer):
"""Abstract GenBank consumer providing useful general functions. This just helps to eliminate some duplication in things that most GenBank consumers want to do. """# Special keys in GenBank records that we should remove spaces from# For instance, \translation keys have values which are proteins and# should have spaces and newlines removed from them. This class# attribute gives us more control over specific formatting problems.
remove_space_keys = ["translation"]
def __init__(self):
pass00226def _split_keywords(self, keyword_string):
"""Split a string of keywords into a nice clean list. """# process the keywords into a python listif keyword_string[-1] == '.':
keywords = keyword_string[:-1]
else:
keywords = keyword_string
keyword_list = keywords.split(';')
clean_keyword_list = [x.strip() for x in keyword_list]
return clean_keyword_list
00238def _split_accessions(self, accession_string):
"""Split a string of accession numbers into a list. """# first replace all line feeds with spaces# Also, EMBL style accessions are split with ';'
accession = accession_string.replace("\n", " ").replace(";"," ")
return [x.strip() for x in accession.split(' ')]
00247def _split_taxonomy(self, taxonomy_string):
"""Split a string with taxonomy info into a list. """if taxonomy_string[-1] == '.':
tax_info = taxonomy_string[:-1]
else:
tax_info = taxonomy_string
tax_list = tax_info.split(';')
new_tax_list = []
for tax_item in tax_list:
new_items = tax_item.split("\n")
new_tax_list.extend(new_items)
while''in new_tax_list:
new_tax_list.remove('')
clean_tax_list = [x.strip() for x in new_tax_list]
return clean_tax_list
00265def _clean_location(self, location_string):
"""Clean whitespace out of a location string. The location parser isn't a fan of whitespace, so we clean it out before feeding it into the parser. """import string
location_line = location_string
for ws in string.whitespace:
location_line = location_line.replace(ws, '')
return location_line
00278def _remove_newlines(self, text):
"""Remove any newlines in the passed text, returning the new string. """# get rid of newlines in the qualifier value
newlines = ["\n", "\r"]
for ws in newlines:
text = text.replace(ws, "")
return text
00288def _normalize_spaces(self, text):
"""Replace multiple spaces in the passed text with single spaces. """# get rid of excessive spaces
text_parts = text.split(" ")
text_parts = filter(None, text_parts)
return' '.join(text_parts)
00296def _remove_spaces(self, text):
"""Remove all spaces from the passed text. """return text.replace(" ", "")
00301def _convert_to_python_numbers(self, start, end):
"""Convert a start and end range to python notation. In GenBank, starts and ends are defined in "biological" coordinates, where 1 is the first base and [i, j] means to include both i and j. In python, 0 is the first base and [i, j] means to include i, but not j. So, to convert "biological" to python coordinates, we need to subtract 1 from the start, and leave the end and things should be converted happily. """
new_start = start - 1
new_end = end
return new_start, new_end
00319class _FeatureConsumer(_BaseGenBankConsumer):
"""Create a SeqRecord object with Features to return. Attributes: o use_fuzziness - specify whether or not to parse with fuzziness in feature locations. o feature_cleaner - a class that will be used to provide specialized cleaning-up of feature values. """def __init__(self, use_fuzziness, feature_cleaner = None):
from Bio.SeqRecord import SeqRecord
_BaseGenBankConsumer.__init__(self)
self.data = SeqRecord(None, id = None)
self.data.id = None
self._use_fuzziness = use_fuzziness
self._feature_cleaner = feature_cleaner
self._seq_type = ''
self._seq_data = []
self._current_ref = None
self._cur_feature = None
self._cur_qualifier_key = None
self._cur_qualifier_value = None00344def locus(self, locus_name):
"""Set the locus name is set as the name of the Sequence. """
self.data.name = locus_name
def size(self, content):
pass00352def residue_type(self, type):
"""Record the sequence type so we can choose an appropriate alphabet. """
self._seq_type = type
def data_file_division(self, division):
self.data.annotations['data_file_division'] = division
def date(self, submit_date):
self.data.annotations['date'] = submit_date
00363def definition(self, definition):
"""Set the definition as the description of the sequence. """
self.data.description = definition
00368def accession(self, acc_num):
"""Set the accession number as the id of the sequence. If we have multiple accession numbers, the first one passed is used. """
new_acc_nums = self._split_accessions(acc_num)
# if we haven't set the id information yet, add the first acc numif self.data.id isNone:
if len(new_acc_nums) > 0:
self.data.id = new_acc_nums[0]
def nid(self, content):
self.data.annotations['nid'] = content
def pid(self, content):
self.data.annotations['pid'] = content
00387def version(self, version_id):
"""Set the version to overwrite the id. Since the verison provides the same information as the accession number, plus some extra info, we set this as the id if we have a version. """
self.data.id = version_id
def db_source(self, content):
self.data.annotations['db_source'] = content.rstrip()
def gi(self, content):
self.data.annotations['gi'] = content
def keywords(self, content):
self.data.annotations['keywords'] = self._split_keywords(content)
def segment(self, content):
self.data.annotations['segment'] = content
def source(self, content):
if content[-1] == '.':
source_info = content[:-1]
else:
source_info = content
self.data.annotations['source'] = source_info
def organism(self, content):
self.data.annotations['organism'] = content
def taxonomy(self, content):
self.data.annotations['taxonomy'] = self._split_taxonomy(content)
00421def reference_num(self, content):
"""Signal the beginning of a new reference object. """from Bio.SeqFeature import Reference
# if we have a current reference that hasn't been added to# the list of references, add it.if self._current_refisnotNone:
self.data.annotations['references'].append(self._current_ref)
else:
self.data.annotations['references'] = []
self._current_ref = Reference()
00434def reference_bases(self, content):
"""Attempt to determine the sequence region the reference entails. Possible types of information we may have to deal with: (bases 1 to 86436) (sites) (bases 1 to 105654; 110423 to 111122) 1 (residues 1 to 182) """# first remove the parentheses or other junk
ref_base_info = content[1:-1]
all_locations = []
# parse if we've got 'bases' and 'to'if ref_base_info.find('bases') != -1 and \
ref_base_info.find('to') != -1:
# get rid of the beginning 'bases'
ref_base_info = ref_base_info[5:]
locations = self._split_reference_locations(ref_base_info)
all_locations.extend(locations)
elif (ref_base_info.find("residues") >= 0 and
ref_base_info.find("to") >= 0):
residues_start = ref_base_info.find("residues")
# get only the information after "residues"
ref_base_info = ref_base_info[(residues_start + len("residues ")):]
locations = self._split_reference_locations(ref_base_info)
all_locations.extend(locations)
# make sure if we are not finding information then we have# the string 'sites' or the string 'bases'elif (ref_base_info == 'sites'or
ref_base_info.strip() == 'bases'):
pass# otherwise raise an errorelse:
raise ValueError("Could not parse base info %s in record %s" %
(ref_base_info, self.data.id))
self._current_ref.location = all_locations
00475def _split_reference_locations(self, location_string):
"""Get reference locations out of a string of reference information The passed string should be of the form: 1 to 20; 20 to 100 This splits the information out and returns a list of location objects based on the reference locations. """from Bio import SeqFeature
# split possibly multiple locations using the ';'
all_base_info = location_string.split(';')
new_locations = []
for base_info in all_base_info:
start, end = base_info.split('to')
new_start, new_end = \
self._convert_to_python_numbers(int(start.strip()),
int(end.strip()))
this_location = SeqFeature.FeatureLocation(new_start, new_end)
new_locations.append(this_location)
return new_locations
def authors(self, content):
self._current_ref.authors = content
def consrtm(self, content):
self._current_ref.consrtm = content
def title(self, content):
self._current_ref.title = content
def journal(self, content):
self._current_ref.journal = content
def medline_id(self, content):
self._current_ref.medline_id = content
def pubmed_id(self, content):
self._current_ref.pubmed_id = content
def remark(self, content):
self._current_ref.comment = content
def comment(self, content):
try :
self.data.annotations['comment'] += "\n" + "\n".join(content)
except KeyError :
self.data.annotations['comment'] = "\n".join(content)
00526def features_line(self, content):
"""Get ready for the feature table when we reach the FEATURE line. """
self.start_feature_table()
00531def start_feature_table(self):
"""Indicate we've got to the start of the feature table. """# make sure we've added on our last reference objectif self._current_refisnotNone:
self.data.annotations['references'].append(self._current_ref)
self._current_ref = None00539def _add_feature(self):
"""Utility function to add a feature to the SeqRecord. This does all of the appropriate checking to make sure we haven't left any info behind, and that we are only adding info if it exists. """if self._cur_feature:
# if we have a left over qualifier, add it to the qualifiers# on the current feature
self._add_qualifier()
self._cur_qualifier_key = ''
self._cur_qualifier_value = ''
self.data.features.append(self._cur_feature)
def feature_key(self, content):
from Bio import SeqFeature
# if we already have a feature, add it on
self._add_feature()
# start a new feature
self._cur_feature = SeqFeature.SeqFeature()
self._cur_feature.type = content
# assume positive strand to start with if we have DNA or cDNA# (labelled as mRNA). The complement in the location will # change this later if something is on the reverse strandif self._seq_type.find("DNA") >= 0 or self._seq_type.find("mRNA") >= 0:
self._cur_feature.strand = 1
00570def location(self, content):
"""Parse out location information from the location string. This uses Andrew's nice spark based parser to do the parsing for us, and translates the results of the parse into appropriate Location objects. """from Bio.GenBank import LocationParser
# --- first preprocess the location for the spark parser# we need to clean up newlines and other whitespace inside# the location before feeding it to the parser.# locations should have no whitespace whatsoever based on the# grammer
location_line = self._clean_location(content)
# Older records have junk like replace(266,"c") in the# location line. Newer records just replace this with# the number 266 and have the information in a more reasonable# place. So we'll just grab out the number and feed this to the# parser. We shouldn't really be losing any info this way.if location_line.find('replace') != -1:
comma_pos = location_line.find(',')
location_line = location_line[8:comma_pos]
# feed everything into the scanner and parsertry:
parse_info = \
LocationParser.parse(LocationParser.scan(location_line))
# spark raises SystemExit errors when parsing failsexcept SystemExit:
raise LocationParserError(location_line)
# print "parse_info:", repr(parse_info)# add the parser information the current feature
self._set_location_info(parse_info, self._cur_feature)
00608def _set_function(self, function, cur_feature):
"""Set the location information based on a function. This handles all of the location functions like 'join', 'complement' and 'order'. Arguments: o function - A LocationParser.Function object specifying the function we are acting on. o cur_feature - The feature to add information to. """from Bio import SeqFeature
from Bio.GenBank import LocationParser
assert isinstance(function, LocationParser.Function), \
"Expected a Function object, got %s" % function
if function.name == "complement":
# mark the current feature as being on the opposite strand
cur_feature.strand = -1
# recursively deal with whatever is left inside the complementfor inner_info in function.args:
self._set_location_info(inner_info, cur_feature)
# deal with functions that have multipe internal segments that# are connected somehow.# join and order are current documented functions.# one-of is something I ran across in old files. Treating it# as a sub sequence feature seems appropriate to me.# bond is some piece of junk I found in RefSeq files. I have# no idea how to interpret it, so I jam it in hereelif (function.name == "join"or function.name == "order"or
function.name == "one-of"or function.name == "bond"):
self._set_ordering_info(function, cur_feature)
elif (function.name == "gap"):
assert len(function.args) == 1, \
"Unexpected number of arguments in gap %s" % function.args
# make the cur information location a gap object
position = self._get_position(function.args[0].local_location)
cur_feature.location = SeqFeature.PositionGap(position)
else:
raise ValueError("Unexpected function name: %s" % function.name)
00649def _set_ordering_info(self, function, cur_feature):
"""Parse a join or order and all of the information in it. This deals with functions that order a bunch of locations, specifically 'join' and 'order'. The inner locations are added as subfeatures of the top level feature """from Bio import SeqFeature
# for each inner element, create a sub SeqFeature within the# current feature, then get the information for this featurefor inner_element in function.args:
new_sub_feature = SeqFeature.SeqFeature()
# inherit the type from the parent
new_sub_feature.type = cur_feature.type
# add the join or order info to the location_operator
cur_feature.location_operator = function.name
new_sub_feature.location_operator = function.name
# inherit references and strand from the parent feature
new_sub_feature.ref = cur_feature.ref
new_sub_feature.ref_db = cur_feature.ref_db
new_sub_feature.strand = cur_feature.strand
# set the information for the inner element
self._set_location_info(inner_element, new_sub_feature)
# now add the feature to the sub_features
cur_feature.sub_features.append(new_sub_feature)
# set the location of the top -- this should be a combination of# the start position of the first sub_feature and the end position# of the last sub_feature# these positions are already converted to python coordinates # (when the sub_features were added) so they don't need to# be converted again
feature_start = cur_feature.sub_features[0].location.start
feature_end = cur_feature.sub_features[-1].location.end
cur_feature.location = SeqFeature.FeatureLocation(feature_start,
feature_end)
00689def _set_location_info(self, parse_info, cur_feature):
"""Set the location information for a feature from the parse info. Arguments: o parse_info - The classes generated by the LocationParser. o cur_feature - The feature to add the information to. """from Bio.GenBank import LocationParser
# base case -- we are out of informationif parse_info isNone:
return# parse a location -- this is another base_case -- we assume# we have no information after a single locationelif isinstance(parse_info, LocationParser.AbsoluteLocation):
self._set_location(parse_info, cur_feature)
return# parse any of the functions (join, complement, etc)elif isinstance(parse_info, LocationParser.Function):
self._set_function(parse_info, cur_feature)
# otherwise we are stuck and should raise an errorelse:
raise ValueError("Could not parse location info: %s"
% parse_info)
00713def _set_location(self, location, cur_feature):
"""Set the location information for a feature. Arguments: o location - An AbsoluteLocation object specifying the info about the location. o cur_feature - The feature to add the information to. """# check to see if we have a cross reference to another accession# ie. U05344.1:514..741if location.path isnotNone:
cur_feature.ref = location.path.accession
cur_feature.ref_db = location.path.database
# now get the actual location information
cur_feature.location = self._get_location(location.local_location)
00729def _get_location(self, range_info):
"""Return a (possibly fuzzy) location from a Range object. Arguments: o range_info - A location range (ie. something like 67..100). This may also be a single position (ie 27). This returns a FeatureLocation object. If parser.use_fuzziness is set at one, the positions for the end points will possibly be fuzzy. """from Bio import SeqFeature
from Bio.GenBank import LocationParser
# check if we just have a single baseifnot(isinstance(range_info, LocationParser.Range)):
pos = self._get_position(range_info)
# move the single position back one to be consistent with how# python indexes numbers (starting at 0)
pos.position = pos.position - 1
return SeqFeature.FeatureLocation(pos, pos)
# otherwise we need to get both sides of the rangeelse:
# get *Position objects for the start and end
start_pos = self._get_position(range_info.low)
end_pos = self._get_position(range_info.high)
start_pos.position, end_pos.position = \
self._convert_to_python_numbers(start_pos.position,
end_pos.position)
return SeqFeature.FeatureLocation(start_pos, end_pos)
00761def _get_position(self, position):
"""Return a (possibly fuzzy) position for a single coordinate. Arguments: o position - This is a LocationParser.* object that specifies a single coordinate. We will examine the object to determine the fuzziness of the position. This is used with _get_location to parse out a location of any end_point of arbitrary fuzziness. """from Bio import SeqFeature
from Bio.GenBank import LocationParser
# case 1 -- just a normal numberif (isinstance(position, LocationParser.Integer)):
final_pos = SeqFeature.ExactPosition(position.val)
# case 2 -- we've got a > signelif isinstance(position, LocationParser.LowBound):
final_pos = SeqFeature.AfterPosition(position.base.val)
# case 3 -- we've got a < signelif isinstance(position, LocationParser.HighBound):
final_pos = SeqFeature.BeforePosition(position.base.val)
# case 4 -- we've got 100^101elif isinstance(position, LocationParser.Between):
final_pos = SeqFeature.BetweenPosition(position.low.val,
position.high.val)
# case 5 -- we've got (100.101)elif isinstance(position, LocationParser.TwoBound):
final_pos = SeqFeature.WithinPosition(position.low.val,
position.high.val)
# case 6 -- we've got a one-of(100, 110) locationelif isinstance(position, LocationParser.Function) and \
position.name == "one-of":
# first convert all of the arguments to positions
position_choices = []
for arg in position.args:
# we only handle AbsoluteLocations with no path# right now. Not sure if other cases will pop upassert isinstance(arg, LocationParser.AbsoluteLocation), \
"Unhandled Location type %r" % arg
assert arg.path isNone, "Unhandled path in location"
position = self._get_position(arg.local_location)
position_choices.append(position)
final_pos = SeqFeature.OneOfPosition(position_choices)
# if it is none of these cases we've got a problem!else:
raise ValueError("Unexpected LocationParser object %r" %
position)
# if we are using fuzziness return what we've gotif self._use_fuzziness:
return final_pos
# otherwise return an ExactPosition equivalentelse:
return SeqFeature.ExactPosition(final_pos.location)
00817def _add_qualifier(self):
"""Add a qualifier to the current feature without loss of info. If there are multiple qualifier keys with the same name we would lose some info in the dictionary, so we append a unique number to the end of the name in case of conflicts. """# if we've got a key from before, add it to the dictionary of# qualifiersif self._cur_qualifier_key:
key = self._cur_qualifier_key
value = "".join(self._cur_qualifier_value)
if self._feature_cleanerisnotNone:
value = self._feature_cleaner.clean_value(key, value)
# if the qualifier name exists, append the valueif key in self._cur_feature.qualifiers:
self._cur_feature.qualifiers[key].append(value)
# otherwise start a new list of the key with its valueselse:
self._cur_feature.qualifiers[key] = [value]
00838def feature_qualifier_name(self, content_list):
"""When we get a qualifier key, use it as a dictionary key. We receive a list of keys, since you can have valueless keys such as /pseudo which would be passed in with the next key (since no other tags separate them in the file) """for content in content_list:
# add a qualifier if we've got one
self._add_qualifier()
# remove the / and = from the qualifier if they're present
qual_key = content.replace('/', '')
qual_key = qual_key.replace('=', '')
qual_key = qual_key.strip()
self._cur_qualifier_key = qual_key
self._cur_qualifier_value = []
def feature_qualifier_description(self, content):
# get rid of the quotes surrounding the qualifier if we've got 'em
qual_value = content.replace('"', '')
self._cur_qualifier_value.append(qual_value)
00863def contig_location(self, content):
"""Deal with a location of CONTIG information. """from Bio import SeqFeature
# add a last feature if is hasn't been added,# so that we don't overwrite it
self._add_feature()
# make a feature to add the information to
self._cur_feature = SeqFeature.SeqFeature()
self._cur_feature.type = "contig"# now set the location on the feature using the standard# location handler
self.location(content)
# add the contig information to the annotations and get rid# of the feature to prevent it from being added to the feature table
self.data.annotations["contig"] = self._cur_feature
self._cur_feature = Nonedef origin_name(self, content):
passdef base_count(self, content):
passdef base_number(self, content):
pass00892def sequence(self, content):
"""Add up sequence information as we get it. To try and make things speedier, this puts all of the strings into a list of strings, and then uses string.join later to put them together. Supposedly, this is a big time savings """
new_seq = content.replace(' ', '')
new_seq = new_seq.upper()
self._seq_data.append(new_seq)
00904def record_end(self, content):
"""Clean up when we've finished the record. """from Bio import Alphabet
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq
# add the last feature in the table which hasn't been added yet
self._add_feature()
# add the sequence information# first, determine the alphabet# we default to an generic alphabet if we don't have a# seq type or have strange sequence information.
seq_alphabet = Alphabet.generic_alphabet
if self._seq_type:
# mRNA is really also DNA, since it is actually cDNAif self._seq_type.find('DNA') != -1 or \
self._seq_type.find('mRNA') != -1:
seq_alphabet = IUPAC.ambiguous_dna
# are there every really RNA sequences in GenBank?elif self._seq_type.find('RNA') != -1:
seq_alphabet = IUPAC.ambiguous_rna
elif self._seq_type == "PROTEIN":
seq_alphabet = IUPAC.protein # or extended protein?# work around ugly GenBank records which have circular or# linear but no indication of sequence typeelif self._seq_typein ["circular", "linear"]:
pass# we have a bug if we get hereelse:
raise ValueError("Could not determine alphabet for seq_type %s"
% self._seq_type)
# now set the sequence
sequence = "".join(self._seq_data)
self.data.seq = Seq(sequence, seq_alphabet)
00942class _RecordConsumer(_BaseGenBankConsumer):
"""Create a GenBank Record object from scanner generated information. """def __init__(self):
_BaseGenBankConsumer.__init__(self)
import Record
self.data = Record.Record()
self._seq_data = []
self._cur_reference = None
self._cur_feature = None
self._cur_qualifier = Nonedef locus(self, content):
self.data.locus = content
def size(self, content):
self.data.size = content
def residue_type(self, content):
self.data.residue_type = content
def data_file_division(self, content):
self.data.data_file_division = content
def date(self, content):
self.data.date = content
def definition(self, content):
self.data.definition = content
def accession(self, content):
new_accessions = self._split_accessions(content)
self.data.accession.extend(new_accessions)
def nid(self, content):
self.data.nid = content
def pid(self, content):
self.data.pid = content
def version(self, content):
self.data.version = content
def db_source(self, content):
self.data.db_source = content.rstrip()
def gi(self, content):
self.data.gi = content
def keywords(self, content):
self.data.keywords = self._split_keywords(content)
def segment(self, content):
self.data.segment = content
def source(self, content):
self.data.source = content
def organism(self, content):
self.data.organism = content
def taxonomy(self, content):
self.data.taxonomy = self._split_taxonomy(content)
01007def reference_num(self, content):
"""Grab the reference number and signal the start of a new reference. """# check if we have a reference to addif self._cur_referenceisnotNone:
self.data.references.append(self._cur_reference)
self._cur_reference = Record.Reference()
self._cur_reference.number = content
def reference_bases(self, content):
self._cur_reference.bases = content
def authors(self, content):
self._cur_reference.authors = content
def consrtm(self, content):
self._cur_reference.consrtm = content
def title(self, content):
self._cur_reference.title = content
def journal(self, content):
self._cur_reference.journal = content
def medline_id(self, content):
self._cur_reference.medline_id = content
def pubmed_id(self, content):
self._cur_reference.pubmed_id = content
def remark(self, content):
self._cur_reference.remark = content
def comment(self, content):
self.data.comment += "\n".join(content)
01044def primary_ref_line(self,content):
"""Data for the PRIMARY line"""
self.data.primary.append(content)
def primary(self,content):
pass01051def features_line(self, content):
"""Get ready for the feature table when we reach the FEATURE line. """
self.start_feature_table()
01056def start_feature_table(self):
"""Signal the start of the feature table. """# we need to add on the last referenceif self._cur_referenceisnotNone:
self.data.references.append(self._cur_reference)
01063def feature_key(self, content):
"""Grab the key of the feature and signal the start of a new feature. """# first add on feature information if we've got any
self._add_feature()
self._cur_feature = Record.Feature()
self._cur_feature.key = content
01072def _add_feature(self):
"""Utility function to add a feature to the Record. This does all of the appropriate checking to make sure we haven't left any info behind, and that we are only adding info if it exists. """if self._cur_featureisnotNone:
# if we have a left over qualifier, add it to the qualifiers# on the current featureif self._cur_qualifierisnotNone:
self._cur_feature.qualifiers.append(self._cur_qualifier)
self._cur_qualifier = None
self.data.features.append(self._cur_feature)
def location(self, content):
self._cur_feature.location = self._clean_location(content)
01091def feature_qualifier_name(self, content_list):
"""Deal with qualifier names We receive a list of keys, since you can have valueless keys such as /pseudo which would be passed in with the next key (since no other tags separate them in the file) """for content in content_list:
# the record parser keeps the /s -- add them if we don't have 'emif content.find("/") != 0:
content = "/%s" % content
# add on a qualifier if we've got oneif self._cur_qualifierisnotNone:
self._cur_feature.qualifiers.append(self._cur_qualifier)
self._cur_qualifier = Record.Qualifier()
self._cur_qualifier.key = content
def feature_qualifier_description(self, content):
# if we have info then the qualifier key should have a ='sif self._cur_qualifier.key.find("=") == -1:
self._cur_qualifier.key = "%s=" % self._cur_qualifier.key
cur_content = self._remove_newlines(content)
# remove all spaces from the value if it is a type where spaces# are not importantfor remove_space_key in self.__class__.remove_space_keys:
if self._cur_qualifier.key.find(remove_space_key) >= 0:
cur_content = self._remove_spaces(cur_content)
self._cur_qualifier.value = self._normalize_spaces(cur_content)
def base_count(self, content):
self.data.base_counts = content
def origin_name(self, content):
self.data.origin = content
01127def contig_location(self, content):
"""Signal that we have contig information to add to the record. """
self.data.contig = self._clean_location(content)
01132def sequence(self, content):
"""Add sequence information to a list of sequence strings. This removes spaces in the data and uppercases the sequence, and then adds it to a list of sequences. Later on we'll join this list together to make the final sequence. This is faster than adding on the new string every time. """
new_seq = content.replace(' ', '')
self._seq_data.append(new_seq.upper())
01143def record_end(self, content):
"""Signal the end of the record and do any necessary clean-up. """# add together all of the sequence parts to create the# final sequence string
self.data.sequence = "".join(self._seq_data)
# add on the last feature
self._add_feature()
def _strip_and_combine(line_list):
"""Combine multiple lines of content separated by spaces. This function is used by the EventGenerator callback function to combine multiple lines of information. The lines are first stripped to remove whitepsace, and then combined so they are separated by a space. This is a simple minded way to combine lines, but should work for most cases. """# first strip out extra whitespace
stripped_line_list = [x.strip() for x in line_list]
# now combine everything with spacesreturn' '.join(stripped_line_list)
def index_file(filename, indexname, rec2key = None, use_berkeley = 0):
"""Index a GenBank file to prepare it for use as a dictionary. Arguments: filename - The name of the GenBank file to be indexed. indexname - The name of the index to create rec2key - A reference to a function object which, when called with a SeqRecord object, will return a key to be used for the record. If no function is specified then the records will be indexed by the 'id' attribute of the SeqRecord (the versioned GenBank id). use_berkeley - specifies whether to use the BerkeleyDB indexer, which uses the bsddb3 wrappers around the embedded database Berkeley DB. By default, the standard flat file (non-Berkeley) indexes are used. """if rec2key:
indexer = SimpleSeqRecord.FunctionIndexer(rec2key)
else:
indexer = SimpleSeqRecord.SimpleIndexer()
if use_berkeley:
SimpleSeqRecord.create_berkeleydb([filename], indexname, indexer)
else:
SimpleSeqRecord.create_flatdb([filename], indexname, indexer)
01191class NCBIDictionary:
"""Access GenBank using a read-only dictionary interface. """
VALID_DATABASES = ['nucleotide', 'protein', 'genome']
VALID_FORMATS = ['genbank', 'fasta']
01196def __init__(self, database, format, parser = None):
"""Initialize an NCBI dictionary to retrieve sequences. Create a new Dictionary to access GenBank. Valid values for database are 'nucleotide' and 'protein'. Valid values for format are 'genbank' (for nucleotide genbank and protein genpept) and 'fasta'. dely and retmax are old options kept only for compatibility -- do not bother to set them. parser is an optional parser object to change the results into another form. If unspecified, then the raw contents of the file will be returned. """
self.parser = parser
if database notin self.__class__.VALID_DATABASES:
raise ValueError("Invalid database %s, should be one of %s" %
(database, self.__class__.VALID_DATABASES))
if format notin self.__class__.VALID_FORMATS:
raise ValueError("Invalid format %s, should be one of %s" %
(format, self.__class__.VALID_FORMATS))
if format == 'fasta':
self.db = db["fasta-sequence-eutils"]
elif format == 'genbank':
if database == 'nucleotide':
self.db = db["nucleotide-genbank-eutils"]
elif database == 'protein':
self.db = db["protein-genbank-eutils"]
elif database == 'genome':
self.db = db["genome-genbank-eutils"]
def __len__(self):
raise NotImplementedError, "GenBank contains lots of entries"def clear(self):
raise NotImplementedError, "This is a read-only dictionary"def __setitem__(self, key, item):
raise NotImplementedError, "This is a read-only dictionary"def update(self):
raise NotImplementedError, "This is a read-only dictionary"def copy(self):
raise NotImplementedError, "You don't need to do this..."def keys(self):
raise NotImplementedError, "You don't really want to do this..."def items(self):
raise NotImplementedError, "You don't really want to do this..."def values(self):
raise NotImplementedError, "You don't really want to do this..."01244def has_key(self, id):
"""S.has_key(id) -> bool"""try:
self[id]
except KeyError:
return 0
return 1
def get(self, id, failobj=None):
try:
return self[id]
except KeyError:
return failobj
raise"How did I get here?"01259def __getitem__(self, id):
"""Return the GenBank entry specified by the GenBank ID. Raises a KeyError if there's an error. """
handle = self.db[id]
# Parse the record if a parser was passed in.if self.parserisnotNone:
return self.parser.parse(handle)
return handle.read()
def search_for(search, database='nucleotide',
reldate=None, mindate=None, maxdate=None,
start_id = 0, max_ids = 50000000):
"""search_for(search[, reldate][, mindate][, maxdate] [, batchsize][, delay][, callback_fn][, start_id][, max_ids]) -> ids Search GenBank and return a list of the GenBank identifiers (gi's) that match the criteria. search is the search string used to search the database. Valid values for database are 'nucleotide', 'protein', 'popset' and 'genome'. reldate is the number of dates prior to the current date to restrict the search. mindate and maxdate are the dates to restrict the search, e.g. 2002/01/01. start_id is the number to begin retrieval on. max_ids specifies the maximum number of id's to retrieve. batchsize, delay and callback_fn are old parameters for compatibility -- do not set them. """# deal with dates
date_restrict = Noneif reldate:
date_restrict = EUtils.WithinNDays(reldate)
elif mindate:
date_restrict = EUtils.DateRange(mindate, maxdate)
eutils_client = DBIdsClient.DBIdsClient()
db_ids = eutils_client.search(search, database, daterange = date_restrict,
retstart = start_id, retmax = max_ids)
ids = []
for db_id in db_ids:
ids.append(db_id.dbids.ids[0])
return ids
def download_many(ids, database = 'nucleotide'):
"""download_many(ids, database) -> handle of results Download many records from GenBank. ids is a list of gis or accessions. callback_fn, broken_fn, delay, faildelay, batchsize, parser are old parameter for compatibility. They should not be used. """
db_ids = DBIds(database, ids)
if database in ['nucleotide']:
format = 'gb'elif database in ['protein']:
format = 'gp'else:
raise ValueError("Unexpected database: %s" % database)
eutils_client = DBIdsClient.from_dbids(db_ids)
result_handle = eutils_client.efetch(retmode = "text", rettype = format)
return cStringIO.StringIO(result_handle.read())